NPASS Compound

Structure

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

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General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC43196

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Potency	3

Activity Type	# Activity
Individual Protein	2
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT249	Individual Protein	Glucocorticoid receptor	Homo sapiens	Potency	n.a.	2238.7	nM	PMID[493384]
NPT103	Individual Protein	Nuclear receptor ROR-gamma	Homo sapiens	Potency	n.a.	4216.3	nM	PMID[493384]
NPT2	Others	Unspecified		Potency	n.a.	28.6	nM	PubChem BioAssay data set

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC43196 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	13998
0.1-0.2	25707
0.2-0.3	2421
0.3-0.4	400
0.4-0.5	100
0.5-0.6	48
0.6-0.7	16
0.7-0.8	4
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.85	High Similarity	NPC321400
0.8182	Intermediate Similarity	NPC237965
0.8182	Intermediate Similarity	NPC318912
0.7826	Intermediate Similarity	NPC304786
0.75	Intermediate Similarity	NPC317724
0.75	Intermediate Similarity	NPC128335
0.72	Intermediate Similarity	NPC272307
0.6957	Remote Similarity	NPC23508
0.6923	Remote Similarity	NPC238135
0.6923	Remote Similarity	NPC88135
0.6818	Remote Similarity	NPC61373
0.68	Remote Similarity	NPC230452
0.68	Remote Similarity	NPC329496
0.6667	Remote Similarity	NPC232172
0.6667	Remote Similarity	NPC184593
0.6667	Remote Similarity	NPC110107
0.6522	Remote Similarity	NPC308490
0.64	Remote Similarity	NPC41485
0.64	Remote Similarity	NPC3693
0.64	Remote Similarity	NPC32280
0.6364	Remote Similarity	NPC327092
0.6364	Remote Similarity	NPC171090
0.625	Remote Similarity	NPC30787
0.625	Remote Similarity	NPC208021
0.625	Remote Similarity	NPC2419
0.6207	Remote Similarity	NPC281883
0.6154	Remote Similarity	NPC127134
0.6154	Remote Similarity	NPC201132
0.6154	Remote Similarity	NPC166804
0.6	Remote Similarity	NPC8368
0.5926	Remote Similarity	NPC143211
0.5926	Remote Similarity	NPC248233
0.5909	Remote Similarity	NPC328688
0.5833	Remote Similarity	NPC327597
0.5833	Remote Similarity	NPC83726
0.5833	Remote Similarity	NPC217229
0.5806	Remote Similarity	NPC140229
0.5769	Remote Similarity	NPC35155
0.5769	Remote Similarity	NPC140389
0.5714	Remote Similarity	NPC317739
0.5714	Remote Similarity	NPC281943
0.5652	Remote Similarity	NPC37493
0.5652	Remote Similarity	NPC173862
0.56	Remote Similarity	NPC203105
0.56	Remote Similarity	NPC8187
0.56	Remote Similarity	NPC7459

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC43196 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	6105
0.1-0.2	2497
0.2-0.3	354
0.3-0.4	145
0.4-0.5	38
0.5-0.6	10
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8333	Intermediate Similarity	NPD8547	Phase 2
0.6207	Remote Similarity	NPD9636	Phase 2
0.6154	Remote Similarity	NPD8992	Approved
0.6154	Remote Similarity	NPD8989	Approved
0.5862	Remote Similarity	NPD901	Approved
0.5714	Remote Similarity	NPD3216	Phase 3
0.5714	Remote Similarity	NPD30	Approved

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data